Interpretive Summary: Replant disease of apple is a major limiting factor to the development of an economically viable orchard on sites previously planted to this crop. Control of soil borne pathogens and parasites is crucial to the successful establishment of new orchards on old orchard sites both in the United States and South Africa. To attain this goal, it is imperative that we possess a clear understanding of the particular pathogen species that contribute to the poor growth of trees newly established on replant sites. In these studies, a number of genera and species of fungi and oomycetes previously shown to be associated with this disease in other regions of the world were recovered from South African orchards exhibiting symptoms of apple replant disease. Among these, oomycetes belonging to the genera Pythium and Phytophthora were among the most commonly isolates and were capable of causing the greatest damage to apple seedlings. Several different species belonging to the fungal genus Fusarium were commonly recovered from affected trees. However, all isolates were almost universally non-pathogenic towards apple, and thus are not implicated in this disease syndrome. This is in agreement with previous studies conducted in the United States and Europe. Fungi belonging to the genus Rhizoctonia were commonly recovered from apple roots, but most isolates were non-pathogenic or demonstrated a low level of virulence towards apple. In total, these findings indicate that oomycetes may function as significant contributors to the development of apple replant disease in South African orchards.

Technical Abstract:
Several species of fungi and oomycetes including Fusarium, Rhizoctonia, Phytophthora and Pythium have been reported as root pathogens of apple where they contribute to a phenomenon known as apple replant disease. In South Africa, very little is known about the specific species in these genera and their pathogenicity toward apple. Therefore, these aspects were investigated along with the development and optimization of qPCR tests for detection and quantification of the most virulent oomycete species. In eight study orchards, the oomycete Phythophthora cactorum was widely distributed, while nine Pythium species were differentially distributed among the orchards. Pythium irregulare was the most widely distributed and the most virulent species along with P. sylvaticum, P. vexans and Phytophthora cactorum. Seven binucleate Rhizoctonia AGs were also differentially distributed among the orchards, with the majority appearing to be non-pathogenic while certain AG-I and AG-F isolates exhibited low virulence on apple. In the genus Fusarium, F. oxysporum was widly distributed, but isolates were non-pathogenic. Fusarium solani and F. avenaceum were less frequently encountered, and as found in previous studies in general were non-pathogenic towards apple. Real time quantitative PCR analysis of DNA extracted from seedling roots inoculated with the most virulent Pythium species (P. irregulare, P. sylvaticum and P. vexans) and the genus Phytophthora were not always reproducible between trials, or isolates of the same species. In general, seedling growth inhibition was associated with the presence of a low amount of pathogen DNA (± 40 fg µl-1 to 2 pg µl-1) in roots. Pythium irregulare, although having the lowest DNA concentrations in roots, was the only species for which a significant negative correlation was found between seedling weight and pathogen DNA concentration.